rs2805657

Variant names:

• chr13-90012528-G-A
• rs2805657

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0463 in 152,052 control chromosomes in the GnomAD database, including 237 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.046 (237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 7022 AN: 151934 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.00676

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0239

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0321

Gnomad OTH AF: 0.0511

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0463 AC: 7036 AN: 152052 Hom.: 237 Cov.: 32 AF XY: 0.0463 AC XY: 3443 AN XY: 74320

Gnomad4 AFR AF: 0.0810

Gnomad4 AMR AF: 0.0367

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.00658

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.0239

Gnomad4 NFE AF: 0.0321

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0356 Hom.: 40

Bravo AF: 0.0480

Asia WGS AF: 0.0330 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2805657; hg19: chr13-90664782;